If a few thousand years ago someone spilt a cup of water somewhere it would not be surprising if no geological record of the event had been found
A second cup of water would not make it a geological event either, nor a third
And whether this water came from within the water cycle or came in to it from a volcano or a comet would also leave no evidence
Just because we have no evidence the flood didn’t occur doesn’t prove it didn’t
Absence of evidence is not evidence of absence
It turns out this is called 'the continuum fallacy' which is easier to understand than it is to spell.
A perfectly good example of 'absence of evidence is not evidence of absence' would be if someone 6,500 years ago spilt a cup of water. The inability of arkeologists to find evidence of it would not prove it didn't happen.
Now comes the principle of induction. Take a heap of straw, remove one single straw, is it still a heap of straw? Yes, therefore you can repeat this without it ever ceasing to be a heap of straw...
You can add another cup of water to the first one spilt and it would remain 'below the radar'.
Just as with the heap of straw, or determining when someone goes bald, the point is not usually well defined, but just because it has not been well-defined doesn't make it non existent.
Total submersion of the planet would leave lots of evidence. The 900,000 year sequence of annual precipitation bands in Antarctica would show it, human societies would come to an end, so for example hieroglyphics before the flood might be very different after, and pyramid building would cease owing to lack of manpower (the Flood came during the pyramid building era though not during the construction of a pyramid)
I am weak on biology but suspect that having just one male and one female ancestor would make a species susceptible to being wiped out by a disease, and leave a clear lack of variation. The situation with cheetahs is similar and it has proven possible to give skin grafts from one cheetah to another without rejection in around 50% of cases. I'd guess the only reason the cheetahs haven't been wiped out by disease is there are so few of them and in such a limited area they have not yet met that particular disease.
The adage 'absence of evidence is not evidence of absence' may apply to spilling a cup of water event but it certainly can not be applied to a global flood even if we have been too lazy to draw a clear dividing line between the two.